Publications by authors named "Amalio Telenti"

100Publications

Author Correction: Treating medical data as a durable asset.

Nat Genet 2020 Oct 8. Epub 2020 Oct 8.

School of Biomedical Informatics, University of Texas Health Science Center at Houston, Houston, TX, USA.

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http://dx.doi.org/10.1038/s41588-020-00734-6DOI Listing
October 2020

Treating medical data as a durable asset.

Nat Genet 2020 Oct 14;52(10):1005-1010. Epub 2020 Sep 14.

School of Biomedical Informatics, University of Texas Health Science Center at Houston, Houston, TX, USA.

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http://dx.doi.org/10.1038/s41588-020-0698-yDOI Listing
October 2020

Advances in Genomics for Drug Development.

Genes (Basel) 2020 Aug 15;11(8). Epub 2020 Aug 15.

Vir Biotechnology, Inc., San Francisco, CA 94158, USA.

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http://dx.doi.org/10.3390/genes11080942DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7465049PMC
August 2020

Regulatory genome variants in human susceptibility to infection.

Hum Genet 2020 Jun 5;139(6-7):759-768. Epub 2019 Dec 5.

Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA.

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http://dx.doi.org/10.1007/s00439-019-02091-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7272256PMC
June 2020

Ranking of non-coding pathogenic variants and putative essential regions of the human genome.

Nat Commun 2019 11 20;10(1):5241. Epub 2019 Nov 20.

Scripps Research Translational Institute, La Jolla, CA, 92037, USA.

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http://dx.doi.org/10.1038/s41467-019-13212-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6868241PMC
November 2019

Machine Learning to Decode Genomics.

Authors:
Amalio Telenti

Clin Chem 2020 01;66(1):45-47

Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA.

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http://dx.doi.org/10.1373/clinchem.2019.308296DOI Listing
January 2020

Functional characterization of 3D protein structures informed by human genetic diversity.

Proc Natl Acad Sci U S A 2019 04 15;116(18):8960-8965. Epub 2019 Apr 15.

The Scripps Research Institute, La Jolla, CA 92037;

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http://www.pnas.org/lookup/doi/10.1073/pnas.1820813116
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http://dx.doi.org/10.1073/pnas.1820813116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6500140PMC
April 2019

Entry of Polarized Effector Cells into Quiescence Forces HIV Latency.

mBio 2019 03 26;10(2). Epub 2019 Mar 26.

Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA

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http://dx.doi.org/10.1128/mBio.00337-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6437053PMC
March 2019

Proteo-Transcriptomic Dynamics of Cellular Response to HIV-1 Infection.

Sci Rep 2019 01 18;9(1):213. Epub 2019 Jan 18.

Institute of Microbiology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland.

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http://dx.doi.org/10.1038/s41598-018-36135-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6338737PMC
January 2019

Response to Whiffin et al.

Am J Hum Genet 2019 01;104(1):186

The Scripps Research Institute, La Jolla, CA 92037, USA. Electronic address:

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http://dx.doi.org/10.1016/j.ajhg.2018.11.011DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6323415PMC
January 2019

A primer on deep learning in genomics.

Nat Genet 2019 01 26;51(1):12-18. Epub 2018 Nov 26.

Scripps Research Translational Institute, La Jolla, CA, USA.

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http://www.nature.com/articles/s41588-018-0295-5
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http://dx.doi.org/10.1038/s41588-018-0295-5DOI Listing
January 2019

Integrating metabolomics with genomics.

Authors:
Amalio Telenti

Pharmacogenomics 2018 12 6;19(18):1377-1381. Epub 2018 Nov 6.

Translational Institute & Department of Integrative Structural & Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.

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https://www.futuremedicine.com/doi/10.2217/pgs-2018-0155
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http://dx.doi.org/10.2217/pgs-2018-0155DOI Listing
December 2018

Deep learning of genomic variation and regulatory network data.

Hum Mol Genet 2018 05;27(R1):R63-R71

Google Inc., Mountain View, CA 94043, USA.

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http://dx.doi.org/10.1093/hmg/ddy115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6499235PMC
May 2018

Comparison of phasing strategies for whole human genomes.

PLoS Genet 2018 04 5;14(4):e1007308. Epub 2018 Apr 5.

J. Craig Venter Institute, La Jolla, California, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1007308DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5903673PMC
April 2018

Rethinking the medical record.

Lancet 2018 03 15;391(10125):1013. Epub 2018 Mar 15.

Scripps Translational Science Institute, The Scripps Research Institute, La Jolla, CA 92037, USA.

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http://dx.doi.org/10.1016/S0140-6736(18)30538-5DOI Listing
March 2018

Acetaminophen (Paracetamol) Use Modifies the Sulfation of Sex Hormones.

EBioMedicine 2018 Feb 15;28:316-323. Epub 2018 Feb 15.

Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA; J. Craig Venter Institute, La Jolla, CA, USA. Electronic address:

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http://dx.doi.org/10.1016/j.ebiom.2018.01.033DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5835573PMC
February 2018

Human gene essentiality.

Nat Rev Genet 2018 Jan 30;19(1):51-62. Epub 2017 Oct 30.

Human Longevity Inc., San Diego, California 92121, USA.

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http://dx.doi.org/10.1038/nrg.2017.75DOI Listing
January 2018

Single-cell analysis identifies cellular markers of the HIV permissive cell.

PLoS Pathog 2017 Oct 26;13(10):e1006678. Epub 2017 Oct 26.

Institute of Microbiology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland.

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https://dx.plos.org/10.1371/journal.ppat.1006678
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http://dx.doi.org/10.1371/journal.ppat.1006678DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5658171PMC
October 2017

Fine population structure analysis method for genomes of many.

Sci Rep 2017 10 3;7(1):12608. Epub 2017 Oct 3.

State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China.

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http://dx.doi.org/10.1038/s41598-017-12319-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5626719PMC
October 2017

The blood DNA virome in 8,000 humans.

PLoS Pathog 2017 03 22;13(3):e1006292. Epub 2017 Mar 22.

Human Longevity Inc., San Diego, California, United States of America.

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http://dx.doi.org/10.1371/journal.ppat.1006292DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5378407PMC
March 2017

Estimating the Respective Contributions of Human and Viral Genetic Variation to HIV Control.

PLoS Comput Biol 2017 02 9;13(2):e1005339. Epub 2017 Feb 9.

School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.

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http://dx.doi.org/10.1371/journal.pcbi.1005339DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5300119PMC
February 2017

The Human Microbiome and Cancer.

Cancer Prev Res (Phila) 2017 Apr 17;10(4):226-234. Epub 2017 Jan 17.

J. Craig Venter Institute (JCVI), Rockville, Maryland.

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http://cancerpreventionresearch.aacrjournals.org/lookup/doi/
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http://dx.doi.org/10.1158/1940-6207.CAPR-16-0249DOI Listing
April 2017

Exploring viral infection using single-cell sequencing.

Virus Res 2017 07 2;239:55-68. Epub 2016 Nov 2.

Institute of Microbiology, University Hospital Center and University of Lausanne, Bugnon 48, CH-1011 Lausanne, Switzerland. Electronic address:

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http://dx.doi.org/10.1016/j.virusres.2016.10.016DOI Listing
July 2017

Protecting genomic data analytics in the cloud: state of the art and opportunities.

BMC Med Genomics 2016 10 13;9(1):63. Epub 2016 Oct 13.

Department of Biomedical Informatics, University of California San Diego, La Jolla, CA, USA.

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http://dx.doi.org/10.1186/s12920-016-0224-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5062944PMC
October 2016

Innate immune defects in HIV permissive cell lines.

Retrovirology 2016 06 27;13(1):43. Epub 2016 Jun 27.

Institute of Microbiology, University Hospital of Lausanne (CHUV) and University of Lausanne, 1011, Lausanne, Switzerland.

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http://dx.doi.org/10.1186/s12977-016-0275-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4924258PMC
June 2016

Dynamics of an Aging Genome.

Cell Metab 2016 Jun;23(6):949-950

Human Longevity Inc., San Diego, CA 92121, USA; J. Craig Venter Institute, La Jolla, CA 92037, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cmet.2016.06.002DOI Listing
June 2016

Identifying Adverse Effects of HIV Drug Treatment and Associated Sentiments Using Twitter.

JMIR Public Health Surveill 2015 Jul-Dec;1(2):e7. Epub 2015 Jul 27.

Center for Infectious Disease DynamicsDepartment of BiologyPenn State UniversityUniversity Park, PAUnited States.

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http://dx.doi.org/10.2196/publichealth.4488DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4869211PMC
May 2016

Single-Cell Genomics for Virology.

Viruses 2016 05 4;8(5). Epub 2016 May 4.

The J. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, CA 92037, USA.

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http://dx.doi.org/10.3390/v8050123DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4885078PMC
May 2016

In Vivo Profiling and Distribution of Known and Novel Phase I and Phase II Metabolites of Efavirenz in Plasma, Urine, and Cerebrospinal Fluid.

Drug Metab Dispos 2016 Jan 9;44(1):151-61. Epub 2015 Nov 9.

Laboratory of Clinical Pharmacology, Service of Biomedicine (M.A., B.T., M.R., L.A.D.), Division of Clinical Pharmacology, Service of Biomedicine (M.A., C.B., T.B.), Service of Infectious Diseases (B.T., M.C.), Institute of Microbiology (A.T., M.R.), and Innovation and Development, Service of Biomedicine (H.H.), University Hospital and University of Lausanne, Lausanne, Switzerland; Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zürich, University of Zürich, Zürich, Switzerland (A.A., H.F.G.); Institute of Medical Virology, University of Zurich, Zurich, Switzerland (H.F.G.); Division of Infectious Diseases, Cantonal Hospital, St. Gallen, Switzerland (P.V.); Laboratory of Virology, University Hospital of Geneva, Geneva, Switzerland (S.Y.); and The J. Craig Venter Institute, La Jolla, California (A.T.)

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http://dx.doi.org/10.1124/dmd.115.065839DOI Listing
January 2016

The Genomic Signature of Population Reconnection Following Isolation: From Theory to HIV.

G3 (Bethesda) 2015 Nov 6;6(1):107-20. Epub 2015 Nov 6.

Department of Ecology and Evolution, University of Lausanne, Lausanne CH-1015, Switzerland School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne CH-1015, Switzerland Institute of Microbiology, University Hospital and University of Lausanne, Lausanne CH-1011, Switzerland.

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http://dx.doi.org/10.1534/g3.115.024208DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4704709PMC
November 2015

Sincell: an R/Bioconductor package for statistical assessment of cell-state hierarchies from single-cell RNA-seq.

Bioinformatics 2015 Oct 22;31(20):3380-2. Epub 2015 Jun 22.

Vital-IT group, SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland, University of Lausanne, 1015 Lausanne, Switzerland and.

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http://dx.doi.org/10.1093/bioinformatics/btv368DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4595899PMC
October 2015

[Medicine faces the digital revolution].

Rev Med Suisse 2015 Apr;11(471):940-3

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April 2015

Genomics of HIV infection.

Authors:
Amalio Telenti

Curr Opin HIV AIDS 2015 Mar;10(2):77-8

aJ. Craig Venter Institute, La Jolla bHuman Longevity Inc., San Diego, California, USA.

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http://dx.doi.org/10.1097/COH.0000000000000140DOI Listing
March 2015

Evolutionary genomics and HIV restriction factors.

Curr Opin HIV AIDS 2015 Mar;10(2):79-83

aUniversity of Lausanne, Lausanne, Switzerland bGenomic Medicine, J. Craig Venter Institute, La Jolla, California, USA cVital-IT group, SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland.

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http://pdfs.journals.lww.com/co-hivandaids/2015/03000/Evolut
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http://content.wkhealth.com/linkback/openurl?sid=WKPTLP:land
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http://dx.doi.org/10.1097/COH.0000000000000138DOI Listing
March 2015

Bioinformatics and HIV latency.

Curr HIV/AIDS Rep 2015 Mar;12(1):97-106

Institute of Microbiology, University Hospital of Lausanne (CHUV), University of Lausanne, Bugnon 48, 1011, Lausanne, Switzerland,

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http://link.springer.com/10.1007/s11904-014-0240-x
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http://dx.doi.org/10.1007/s11904-014-0240-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4369283PMC
March 2015

On genomics, kin, and privacy.

F1000Res 2014 31;3:80. Epub 2014 Mar 31.

Laboratory for Communications and Applications Laboratory, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.

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https://f1000research.com/articles/3-80/v1
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http://dx.doi.org/10.12688/f1000research.3817.1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4168742PMC
September 2014

Disentangling human tolerance and resistance against HIV.

PLoS Biol 2014 Sep 16;12(9):e1001951. Epub 2014 Sep 16.

Global Health Institute, EPF Lausanne, Lausanne, Switzerland; Swiss Institute of Bioinformatics, Lausanne, Switzerland.

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http://dx.doi.org/10.1371/journal.pbio.1001951DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4165755PMC
September 2014

Analysis of stop-gain and frameshift variants in human innate immunity genes.

PLoS Comput Biol 2014 Jul 24;10(7):e1003757. Epub 2014 Jul 24.

Department of Laboratories, University Hospital of Lausanne, Lausanne, Switzerland; University of Lausanne, Lausanne, Switzerland.

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https://dx.plos.org/10.1371/journal.pcbi.1003757
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http://dx.doi.org/10.1371/journal.pcbi.1003757DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4110073PMC
July 2014

HIV: The mixed blessing of interferon.

Authors:
Amalio Telenti

Nature 2014 Jul 9;511(7511):537-8. Epub 2014 Jul 9.

Institute of Microbiology, University Hospital of Lausanne, University of Lausanne, 1011 Lausanne, Switzerland.

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http://www.nature.com/doifinder/10.1038/nature13517
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http://dx.doi.org/10.1038/nature13517DOI Listing
July 2014

HIV-1 capture and transmission by dendritic cells: the role of viral glycolipids and the cellular receptor Siglec-1.

PLoS Pathog 2014 Jul 17;10(7):e1004146. Epub 2014 Jul 17.

AIDS Research Institute IrsiCaixa, Institut d'Investigació en Ciències de la Salut Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, Spain; Universitat de Vic-Universitat Central de Catalunya (UVic-UCC), Vic, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.

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https://dx.plos.org/10.1371/journal.ppat.1004146
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http://dx.doi.org/10.1371/journal.ppat.1004146DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4102576PMC
July 2014

Genomics of host-pathogen interactions.

Curr Opin Immunol 2014 Oct 24;30:32-8. Epub 2014 Jun 24.

Institute of Microbiology, University Hospital, University of Lausanne, Switzerland. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S09527915140008
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http://dx.doi.org/10.1016/j.coi.2014.06.001DOI Listing
October 2014

Dynamics of HIV latency and reactivation in a primary CD4+ T cell model.

PLoS Pathog 2014 May 29;10(5):e1004156. Epub 2014 May 29.

Institute of Microbiology, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland; University of Lausanne, Lausanne, Switzerland.

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http://dx.doi.org/10.1371/journal.ppat.1004156DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4038609PMC
May 2014

Highly pathogenic adapted HIV-1 strains limit host immunity and dictate rapid disease progression.

AIDS 2014 Jun;28(9):1261-72

aAIDS Research Institute -IrsiCaixa-iInstitut d'Investigació en Ciències de la Salut Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, Spain bInstitute of Microbiology, University Hospital Center and University of Lausanne, Lausanne cUniversity Clinic of Infectious Diseases, University Hospital Bern and University of Bern, Bern, Switzerland dUniversidad Complutense de Madrid, Madrid, Spain eMonogram Biosciences, South San Francisco, California, USA fCentre d'Estudis Epidemiològics sobre les Infeccions de Transmissió Sexual i Sida de Catalunya (CEEISCAT), Badalona gBanc de Sang i Teixits, Barcelona hUniversitat de Vic (UVic-UCC), Vic iInstitució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain. *Judith Dalmau and Margalida Rotger contributed equally to this article. †Amalio Talenti, Javier Martinez-Picado and Julia G. Prado contributed equally to the work.

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http://dx.doi.org/10.1097/QAD.0000000000000293DOI Listing
June 2014

GuavaH: a compendium of host genomic data in HIV biology and disease.

Retrovirology 2014 Jan 15;11. Epub 2014 Jan 15.

Institute of Microbiology, University Hospital Lausanne, Lausanne, Switzerland.

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http://retrovirology.biomedcentral.com/articles/10.1186/1742
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http://dx.doi.org/10.1186/1742-4690-11-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3937115PMC
January 2014

A genome-to-genome analysis of associations between human genetic variation, HIV-1 sequence diversity, and viral control.

Elife 2013 Oct 29;2:e01123. Epub 2013 Oct 29.

School of Life Sciences , École Polytechnique Fédérale de Lausanne , Lausanne , Switzerland ; Institute of Microbiology , University Hospital and University of Lausanne , Lausanne , Switzerland ; Research Group of Theoretical Biology and Evolutionary Ecology , Eötvös Loránd University and the Hungarian Academy of Sciences , Budapest , Hungary ; Swiss Institute of Bioinformatics , Lausanne , Switzerland.

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http://dx.doi.org/10.7554/eLife.01123DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3807812PMC
October 2013

HIV and innate immunity - a genomics perspective.

F1000Prime Rep 2013 1;5:29. Epub 2013 Aug 1.

Institute of Microbiology, University Hospital of Lausanne and University of Lausanne Switzerland ; Swiss Institute of Bioinformatics, Lausanne Switzerland.

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http://dx.doi.org/10.12703/P5-29DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3732074PMC
August 2013

A validated assay by liquid chromatography-tandem mass spectrometry for the simultaneous quantification of elvitegravir and rilpivirine in HIV positive patients.

J Mass Spectrom 2013 May;48(5):616-25

Innovation & Development Laboratory, Service of Biomedicine, Centre Hospitalier Universitaire Vaudois, Switzerland.

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http://dx.doi.org/10.1002/jms.3200DOI Listing
May 2013

Efavirenz intoxication due to a new CYP2B6 constellation.

Antivir Ther 2013 2;18(5):739-43. Epub 2013 May 2.

Division of Infectious Diseases and Hospital Epidemiology, University Hospital of Zurich, University of Zurich, Zurich, Switzerland.

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http://dx.doi.org/10.3851/IMP2571DOI Listing
June 2014

Multiplex liquid chromatography-tandem mass spectrometry assay for simultaneous therapeutic drug monitoring of ribavirin, boceprevir, and telaprevir.

Antimicrob Agents Chemother 2013 Jul 29;57(7):3147-58. Epub 2013 Apr 29.

Innovation & Development Laboratory, Centre Hospitalier Universitaire Vaudois, University of Lausanne, Lausanne, Switzerland.

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http://dx.doi.org/10.1128/AAC.00281-13DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3697367PMC
July 2013

Susceptibility and adaptation to human TRIM5α alleles at positive selected sites in HIV-1 capsid.

Virology 2013 Jul 17;441(2):162-70. Epub 2013 Apr 17.

Institute of Microbiology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland.

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http://dx.doi.org/10.1016/j.virol.2013.03.021DOI Listing
July 2013

Contribution of genetic background, traditional risk factors, and HIV-related factors to coronary artery disease events in HIV-positive persons.

Clin Infect Dis 2013 Jul 26;57(1):112-21. Epub 2013 Mar 26.

Institute of Microbiology, University Hospital Center, University of Lausanne, Lausanne, Switzerland.

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http://dx.doi.org/10.1093/cid/cit196DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3669528PMC
July 2013

State of genomics and epigenomics research in the perspective of HIV cure.

Curr Opin HIV AIDS 2013 May;8(3):176-81

Institute of Microbiology, University Hospital of Lausanne, University of Lausanne, Lausanne, Switzerland.

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http://content.wkhealth.com/linkback/openurl?sid=WKPTLP:land
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http://dx.doi.org/10.1097/COH.0b013e32835f7340DOI Listing
May 2013

24 hours in the life of HIV-1 in a T cell line.

PLoS Pathog 2013 Jan 31;9(1):e1003161. Epub 2013 Jan 31.

Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland.

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http://dx.doi.org/10.1371/journal.ppat.1003161DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3561177PMC
January 2013